Return to study ST003182 main page
MB Sample ID: SA346713
Local Sample ID: | Pro_2 |
Subject ID: | SU003301 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU003301 |
Subject Type: | Cultured cells |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Pro_2 | SA346713 | FL040686 | Pro | Treatment |
Pro_2 | SA346713 | FL040686 | lung embryonic fibroblasts | Sample source |
Collection:
Collection ID: | CO003294 |
Collection Summary: | IMR90 primary human diploid lung embryonic fibroblasts were used and cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), L-glutamine, sodium pyruvate, non-essential amino acids, sodium bicarbonate and 1% penicillin-streptomycin under low oxygen tension (2%). |
Sample Type: | Cultured cells |
Treatment:
Treatment ID: | TR003310 |
Treatment Summary: | Stable isotope tracer analysis using 13C6-glucose was conducted in three biologically independent experiments for the following experimental groups: control proliferating cells (Pro), RAS-induced senescent cells via 4-OHT with control shRNA (Sen_shctrl), senescent cells with shRNA targeting HK2 (Sen_shHK2), senescent cells with shRNA targeting HK2 and rescued with wildtype Flag-HK2 (Sen_shHK2_WTHK2), and senescent cells with shRNA targeting HK2 and rescued with mutant Flag-HK2 (Sen_shHK2_MutHK2). The experiments were performed by seeding cells at a density of 3 × 10^5 cells per 6 cm dish and incubating them with 25 mM [13C6]-glucose tracer in glucose-free medium for 30 min. |
Sample Preparation:
Sampleprep ID: | SP003308 |
Sampleprep Summary: | Following incubation, the cells were washed with chilled PBS and incubated with 500 µl of extraction solution (80:20 v/v methanol/water) at 4 °C for 5 minutes. Next, cells were scraped with a polypropylene cell scraper and the extraction solution from each sample was collected, vortexed, and incubated on dry ice for at least 30 min. Then, each sample was centrifuged at maximum speed at 4 °C for 10 minutes, and the resulting supernatant was used for metabolic measurements. |
Combined analysis:
Analysis ID | AN005226 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Thermo Vanquish Horizon UHPLC |
Column | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive HF-X Orbitrap |
Ion Mode | UNSPECIFIED |
Units | Peak Area |
Chromatography:
Chromatography ID: | CH003953 |
Chromatography Summary: | Hydrophilic interaction liquid chromatography (HILIC) was performed at 0.2 ml/min on a ZIC-pHILIC column (2.1 mm × 150 mm, 5 µm particle size, EMD Millipore) at 45 °C. Solvent A was 20 mM ammonium carbonate, 0.1% ammonium hydroxide, pH 9.2, and solvent B was acetonitrile. The gradient was 85% B for 2 min, 85% B to 20% B over 15 min, 20% B to 85% B over 0.1 min, and 85% B for 8.9 min. The autosampler was held at 4 °C. For each analysis, 4 µl of sample was injected. |
Instrument Name: | Thermo Vanquish Horizon UHPLC |
Column Name: | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
Column Temperature: | 45 |
Flow Gradient: | 85% B for 2 min, 85% B to 20% B over 15 min, 20% B to 85% B over 0.1 min, and 85% B for 8.9 min |
Flow Rate: | 0.2 ml/min |
Solvent A: | 100% water; 20 mM ammonium carbonate; 5 µM medronic acid; 0.1% ammonium hydroxide |
Solvent B: | 100% acetonitrile |
Chromatography Type: | HILIC |
MS:
MS ID: | MS004959 |
Analysis ID: | AN005226 |
Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | The following parameters were used for the MS analysis: sheath gas flow rate, 40; auxiliary gas flow rate, 10; sweep gas flow rate, 2; auxiliary gas heater temperature, 350 °C; spray voltage, 3.5 kV for positive mode and 3.2 kV for negative mode; capillary temperature, 325 °C; and funnel RF level, 40. All samples were analyzed by full MS with polarity switching. Technical injections of an unlabeled sample pool were analyzed throughout the sample sequence. The unlabeled sample pool was also analyzed by data-dependent MS/MS with separate runs for positive and negative ion modes. Full MS scans were acquired at 120,000 resolution with a scan range of 65-975 m/z. Data-dependent MS/MS scans were acquired for the top 10 highest intensity ions at 15,000 resolution with an isolation width of 1.0 m/z and stepped normalized collision energy of 20-40-60. Annotation and quantitation of metabolites and carbon isotopologues with natural isotope abundance correction were performed using Compound Discoverer 3.3 software (Thermo Scientific). Metabolite measurements were normalized based on the protein concentration in the protein pellets. |
Ion Mode: | UNSPECIFIED |